Modomics - A Database of RNA Modifications

pGp
The molecule is shown in a ball-and-stick representation with the following colors for atoms :
⬤ Hydrogen (H): white ⬤ Carbon (C): gray ⬤ Oxygen (O): red ⬤ Phosphorus (P): orange ⬤ Nitrogen (N): blue ⬤ Selenium (Se): gold ⬤ Sulfur (S): yellow
See the molecule on the similarity map

Summary

Full nameguanosine-3',5'-diphosphate
Short namepGp
MODOMICS code new2000033551G
MODOMICS code33551G
Nature of the modified residueNatural
RNAMods codeȺ
Residue unique ID259
Found in RNAYes
Related nucleosides38
RCSB ligands

PGP


Chemical information

Sum formulaC10H10N5O11P2
Type of moietynucleotide
Degeneracynot aplicable
SMILES[C@H]1([n]2cnc3c2nc(nc3=O)N)[C@H](O)[C@H](OP([O-])([O-])=O)[C@@H](COP([O-])([O-])=O)O1
logP-2.5135
TPSA277.33
Number of atoms28
Number of Hydrogen Bond Acceptors 1 (HBA1)12
Number of Hydrogen Bond Acceptors 2 (HBA2)16
Number of Hydrogen Bond Donors (HBD)2
InChIInChI=1S/C10H14N5O11P2/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(26-28(21,22)23)3(25-9)1-24-27(18,19)20/h2-3,5-6,9,16H,1H2,(H2,11,14,17)(H2,18,19,20)(H2,21,22,23)/p-4/t3-,5-,6-,9-/m1/s1
InChIKeyCCJHMJVYJPHPHC-UUOKFMHZSA-J
Search the molecule in external databases ChEMBL  ChemAgora  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)

QM Data:

Dipole Magnitude [D]:53.149263
Energy [Eh]:-2171.63130161559
HOMO [eV]:-8.3115
LUMO [eV]:1.5725
Gap [eV]:9.884

Download QM Data:

Cube   .cube
Charges   charge.txt

Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb


LC-MS Information

Monoisotopic massNone
Average mass438.161
[M+H]+ not available
Product ions not available
Normalized LC elution time * not available
LC elution order/characteristics not available

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

Last modification of this entry: Sept. 15, 2025